scholarly journals Community-Wide Response of the Gut Microbiota to Enteropathogenic Citrobacter rodentium Infection Revealed by Deep Sequencing

2009 ◽  
Vol 77 (10) ◽  
pp. 4668-4678 ◽  
Author(s):  
Christian Hoffmann ◽  
David A. Hill ◽  
Nana Minkah ◽  
Thomas Kirn ◽  
Amy Troy ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Deep Sequencing ◽  
Distal Colon ◽  
Proximal Colon ◽  
Rrna Gene ◽  
Citrobacter Rodentium ◽  
Sequencing Data ◽  
Adaptive Immune ◽  
Gut Microbial Community

ABSTRACT We investigated the spatial and temporal response of the murine gut microbiome to infection with Citrobacter rodentium, an attaching-and-effacing bacterium that provokes innate and adaptive immune responses, resulting in transient bacterial colitis. Previous studies have suggested that C. rodentium-induced inflammation is associated with an increased abundance of Enterobacteriaceae. We report here a deeper analysis of this model using DNA bar coding and 454 pyrosequencing to characterize 101,894 partial 16S rRNA gene sequences from 85 microbial samples from tissue-adhered and luminal bacteria of the cecum, proximal colon, and distal colon, which allowed us to identify previously unappreciated spatial and kinetic changes in multiple bacterial lineages. The deep sequencing data revealed that C. rodentium was most abundantly associated with the cecal mucosa at day 9 postinfection and then diminished in abundance, providing the first reported use of deep sequencing to track a pathogen in vivo through the course of infection. Notable changes were associated with both the mucosally adhered and luminal microbiota at both day 9 and day 14 postinfection. Alterations in abundance were seen for Proteobacteria, Deferribacteres, Clostridia, and others; however, changes in Enterobacteriaceae could be accounted for by the presence of C. rodentium itself, which is a member of this family. The Lactobacillus group decreased in abundance during infection, which may be important for pathogenesis because members of this lineage modulate the composition of the gut microbiota and are used as probiotics. Thus, deep sequencing provides previously inaccessible information on how Citrobacter infection and clearance reshapes the gut microbial community in space and time.

scholarly journals Encapsulated cyclosporine does not change the composition of the human microbiota when assessed ex vivo and in vivo

2020 ◽  
Vol 69 (6) ◽  
pp. 854-863
Author(s):  
Catherine O'Reilly ◽  
Órla O’Sullivan ◽  
Paul D. Cotter ◽  
Paula M. O’Connor ◽  
Fergus Shanahan ◽  
...  
Keyword(s):  
Pilot Study ◽  
Gut Microbiota ◽  
Targeted Delivery ◽  
Healthy Subjects ◽  
Ex Vivo ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Faecal Samples

Introduction. Management of steroid-refractory ulcerative colitis has predominantly involved treatment with systemic cyclosporine A (CyA) and infliximab. Aim. The purpose of this study was to assess the effect of using a colon-targeted delivery system CyA formulation on the composition and functionality of the gut microbiota. Methodology. Ex vivo faecal fermentations from six healthy control subjects were treated with coated minispheres (SmPill) with (+) or without (−) CyA and compared with a non-treated control in a model colon system. In addition, the in vivo effect of the SmPill+CyA formulation was investigated by analysing the gut microbiota in faecal samples collected before the administration of SmPill+CyA and after 7 consecutive days of administration from eight healthy subjects who participated in a pilot study. Results. Analysis of faecal samples by 16S rRNA gene sequencing indicated little variation in the diversity or relative abundance of the microbiota composition before or after treatment with SmPill minispheres with or without CyA ex vivo or with CyA in vivo. Short-chain fatty acid profiles were evaluated using gas chromatography, showing an increase in the concentration of n-butyrate (P=0.02) and acetate (P=0.32) in the faecal fermented samples incubated in the presence of SmPill minispheres with or without CyA. This indicated that increased acetate and butyrate production was attributed to a component of the coated minispheres rather than an effect of CyA on the microbiota. Butyrate and acetate levels also increased significantly (P=0.05 for both) in the faecal samples of healthy individuals following 7 days’ treatment with SmPill+CyA in the pilot study. Conclusion. SmPill minispheres with or without CyA at the clinically relevant doses tested here have negligible direct effects on the gut microbiota composition. Butyrate and acetate production increased, however, in the presence of the beads in an ex vivo model system as well as in vivo in healthy subjects. Importantly, this study also demonstrates the relevance and value of using ex vivo colon models to predict the in vivo impact of colon-targeted drugs directly on the gut microbiota.

scholarly journals Colonisation potential of plantaricin-producing Lactobacillus plantarum SF9C andS-layer-carrying Lactobacillus brevis SF9B among gut microbiota

2020 ◽  
Author(s):  
Katarina Butorac ◽  
Martina Banic ◽  
Jasna Novak ◽  
Andreja Leboš Pavunc ◽  
Ksenija Uroic ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Lactobacillus Plantarum ◽  
Lactobacillus Brevis ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Combined Application ◽  
Probiotic Potential ◽  
Gut Microbiota Composition

Abstract Background: The influence of an S-layer-carrying strain Lactobacillus brevis SF9B and a plantaricin-producing strain Lactobacillus plantarum SF9C on the gut microbiota composition was evaluated in the rats. Considering the probiotic potential of Lb. brevis SF9B, this study aimed to examine the antibacterial activity of Lb. plantarum SF9C and potential for their in vivo colonisation, which could be the basis for the investigation of their synergistic functionality. Results: A plantaricin-encoding cluster was identified in Lb. plantarum SF9C, a strain which efficiently inhibited the growth of Listeria monocytogenes ATCC®19111™ and Staphylococcus aureus 3048. Contrary to the plantaricin-producing SF9C strain, the S-layer-carrying SF9B strain excluded Escherichia coli 3014 and Salmonella enterica serovar Typhimurium FP1 from adhesion to Caco-2 cells. Finally, DGGE analysis of the V2-V3 region of the 16S rRNA gene confirmed the transit of two selected lactobacilli through the gastrointestinal tract (GIT). Microbiome profiling via the Illumina MiSeq platform revealed the prevalence of Lactobacillus spp. in the gut microbiota of rats suggesting their colonisation potential in GIT.Conclusion: The combined application of Lb. plantarum SF9C and Lb. brevis SF9B could influence the intestinal microbiota composition, which is reflected through the increased abundance of Lactobacillus genus, but also through altered abundances of other bacterial genera, either in the model of healthy or aberrant microbiota of rats. The obtained results contributed to the functional aspects of SF9C and SF9B strains which could be incorporated in the probiotic-containing functional foods and therefore have a beneficial influence on the gut microbiota composition.

scholarly journals Yoghurt Consumption is Associated With Transient Changes in the Composition of the Human Gut Microbiome

2020 ◽  
Author(s):  
Caroline Ivanne Le Roy ◽  
Alexander Kurilshikov ◽  
Emily Leeming ◽  
Alessia Visconti ◽  
Ruth Bowyer ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Visceral Fat ◽  
Gut Microbiome ◽  
Body Weight Gain ◽  
Healthy Eating Index ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
Shotgun Metagenomic Sequencing

Abstract Background: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results: According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17±0.34; P = 2.72x10-10) and improved metabolic health characterised by reduced visceral fat (beta = -28.18±11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41±0.051; P = 6.14x10-12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30±0.052; P = 1.49x10-8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed that increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation.Conclusions: Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).

scholarly journals The Effect of Transitioning between Feeding Methods on the Gut Microbiota Dynamics of Yaks on the Qinghai–Tibet Plateau

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1641
Author(s):  
Xiao-Ling Zhang ◽  
Tian-Wei Xu ◽  
Xun-Gang Wang ◽  
Yuan-Yue Geng ◽  
Hong-Jin Liu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
16S Rrna Gene Sequencing ◽  
Tibet Plateau ◽  
Rrna Gene ◽  
Adaptation Period ◽  
Class Level ◽  
Feeding Methods ◽  
Rrna Gene Sequencing ◽  
Gut Microbial Community ◽  
Qinghai Tibet Plateau

Here we aimed to explore the change in yak gut microbiota after transferring yaks from grazing grassland to a feedlot, and determine their diet adaptation period. Five yaks were transferred from winter pasture to an indoor feedlot. Fecal samples were obtained from grazing (G) and feedlot feeding yaks at day 1 (D1), day 4 (D4), day 7 (D7), day 11 (D11), and day 16 (D16). The dynamic variation of the bacterial community was analyzed using 16S rRNA gene sequencing. The results showed that the yak gut microbial community structure underwent significant changes after diet transition. At the phylum and genus levels, most bacteria changed within D1–D11; however, no significant changes were observed from D11–D16. Furthermore, we used random forest to determine the key bacteria (at class level) disturbing gut micro-ecology. The relative abundance of the top four classes (Erysipelotrichia, Gammaproteobacteria, Saccharimonadia, and Coriobacteriia) was highest on D1–D4, and then decreased and plateaued over time. Our results demonstrated that an abrupt adjustment to a diet with high nutrition could influence the gut micro-ecology, which was stabilized within 16 days, thus providing insights into diet adaptation in the yak gut.

scholarly journals Gut microbiota and age shape susceptibility to clostridial enteritis in lorikeets under human care

2021 ◽  
Author(s):  
David Minich ◽  
Christopher Madden ◽  
Mauricio A. Navarro ◽  
Leo Glowacki ◽  
Kristen French-Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Treatment Plan ◽  
Type A ◽  
Toxin Gene ◽  
Sequencing Data ◽  
Intestinal Lesions ◽  
Rhodococcus Fascians ◽  
Human Care ◽  
Gut Microbial Community ◽  
Data Culture

AbstractBackgroundEnteritis is a common cause of morbidity and mortality in lorikeets that can be challenging to diagnose and treat. In this study, we examine gut microbiota in two lorikeet flocks with enteritis (Columbus Zoo and Aquarium – CZA; Denver Zoo - DZ). Since 2012, the CZA flock has experienced repeated outbreaks of enteritis despite extensive diet, husbandry, and clinical modifications. In 2018, both CZA and DZ observed a spike in enteritis. Recent research has revealed that the gut microbiota can influence susceptibility to enteropathogens. We hypothesized that a dysbiosis, or alteration in the gut microbial community, was making some lorikeets more susceptible to enteritis, and our goal was to characterize this dysbiosis and determine the features that predicted susceptibility.ResultsWe employed 16S rRNA sequencing to characterize the cloacal microbiota in lorikeets (CZA n = 67, DZ n = 24) over time. We compared the microbiota of healthy lorikeets, to lorikeets with enteritis, and lorikeets susceptible to enteritis, with “susceptible” being defined as healthy birds that subsequently developed enteritis. Based on sequencing data, culture, and toxin gene detection in intestinal contents, we identified Clostridium perfringens type A (CZA and DZ) and C. colinum (CZA only) at increased relative abundances in birds with enteritis. Histopathology and immunohistochemistry further identified the presence of gram-positive bacilli and C. perfringens, respectively, in the necrotizing intestinal lesions. Finally, using Random Forests and LASSO models, we identified several features (young age and the presence of Rhodococcus fascians and Pseudomonas umsongensis) associated with susceptibility to clostridial enteritis.ConclusionsWe identified C. perfringens type A and C. colinum associated with lorikeet necrohemorrhagic enteritis at CZA and DZ. Susceptibility testing of isolates lead to an updated clinical treatment plan which ultimately resolved the outbreaks at both institutions. This work provides a foundation for understanding gut microbiota features that are permissive to clostridial colonization and host factors (e.g. age, prior infection) that shape responses to infection.

scholarly journals A comprehensive analysis of the microbiota composition and gene expression in colorectal cancer

2019 ◽  
Author(s):  
Qian Zhang ◽  
Huan Zhao ◽  
Dedong Wu ◽  
Dayong Cao ◽  
Wang Ma
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Gut Microbiota ◽  
Bile Secretion ◽  
Colorectal Carcinogenesis ◽  
The Cancer Genome Atlas ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Sequencing Data ◽  
Keywords Colorectal Cancer

Abstract Subject: The dysbiosis of gut microbiota is pivotal in colorectal carcinogenesis. However, the synergy between an altered gut microbiota composition and differential gene expression of specific genes in colorectal cancer (CRC) remains elusive. Method: The gut microbiota dataset with number SRP158779, which contained 19 CRC samples and 19 normal samples, was downloaded from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database. The 16S rRNA gene sequences from this dataset were clustered into operational taxonomic units (OTUs); thereafter, the OTUs that were differentially enriched in CRC were identified and classified, followed by prediction of their functions. Additionally, RNA sequencing data from CRC samples was obtained from The Cancer Genome Atlas project (TCGA), and the differentially expressed genes (DEGs) and enriched pathways were identified. Finally, similar pathways that were significantly enriched in both differential OTUs and DEGs were screened. Key genes related to these pathways were executed the prognosis analysis. Results: The presence of Proteobacteria and Fusobacteria increased considerably in CRC samples; conversely, the abundance of Firmicute and Spirochaetes decreased markedly. In particular, the genera Fusobacterium , Catenibacterium , and Shewanella were detectable in tumor samples. Moreover, 246 DEGs were identified between tumor and normal tissues. Both DEGs and microbiota were involved in bile secretion and steroid hormone biosynthesis pathways. Finally, CYP3A4 and ABCG2 expression in CRC was related to the prognostic outcomes of CRC patients. Conclusion: Identifying the complicated interplay between gut microbiota and the DEGs could help in further understanding the pathogenesis of CRC, and these findings would enable better diagnosis and treatment of CRC patients. Keywords: colorectal cancer, gut microflora, gene expression, pathways enrichment, survival analysis

scholarly journals Genomic Techniques Used to Investigate the Human Gut Microbiota

2021 ◽  
Author(s):  
Akhlash P. Singh
Keyword(s):  
Gut Microbiota ◽  
High Throughput ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Human Gut ◽  
Culture Independent ◽  
Microbe Interactions ◽  
Next Generation Sequencing Ngs ◽  
Lifestyle Related Diseases ◽  
Gut Microbial Community

The human gut is the complex microbial ecosystem comprises more than 100 trillion microbes also known as microbiota. The gut microbiota does not only include about 400–500 types of bacterial strains, but it also contains archaea, bacteriophage, fungi, and protozoa species. In order to complete the characterization of the gut microbial community, we need the help of many culture-dependent and culture-independent genomic technologies. Recently, next-generation sequencing (NGS), mediated metagenomics that rely on 16S rRNA gene amplification, and whole-genome sequencing (WGS) have provided us deep knowledge related to important interactions such as host-microbiota and microbe-microbe interactions under various perturbation inside the gut. But, we still lack complete knowledge related to unique gene products encoded by gut meta-genome. Hence, it required the application of high-throughput “omics-based” methods to support metagenomics. Currently, a combination of high-throughput culturing and microfluidics assays is providing a new method to characterize non-amenable bacterial strains from the gut environment. The recent additions of artificial intelligence and deep learning to the area of microbiome studies have enhanced the capability of identification of thousand microbes simultaneously. Given above, it is necessary to apply new genome editing tools that can be used to design the personalized microflora which can be used to cure lifestyle-related diseases.

scholarly journals A126 RETROGRADE LABELLING OF NODOSE GANGLIA IN VIVO BY FLUORESCENT TRACERS

2020 ◽  
Vol 3 (Supplement_1) ◽  
pp. 146-147
Author(s):  
A A Tashtush ◽  
A E Lomax
Keyword(s):  
Vagus Nerve ◽  
Principal Component ◽  
Distal Colon ◽  
Proximal Colon ◽  
Vagal Afferents ◽  
Sensory Innervation ◽  
Lower Percentage ◽  
Retrograde Labelling ◽  
Nodose Ganglia

Abstract Background The gut-brain axis is a bidirectional connection between the gastrointestinal tract (GI)and the central nervous system. The vagus nerve has been recognized as a principal component of this axis. Vagus nerve plays important role in maintaining homeostasis and normal GI functions, its afferent fibers can detect microbiota metabolites also. Many studies have demonstrated that the upper GI tract receives dense vagal innervation, which decreases distally throughout the tract. However, the distal colon sensory innervation of the vagus nerve remains controversial. Aims To illuminate the extent to which the vagus nerve innervates the colon, to determine whether anatomical evidence exists for double-labeled vagal afferents supplying the proximal and distal colon in the nodose ganglia. Methods C57Bl/6 mice (n=8) were injected in the proximal and distal colon with alternating solutions of retrograde tracers 1.7% Fast blue (FB) and 5% of lipophilic tracer DiI. Animals were left to recover for 10–13 days then underwent cardiac perfusion. Nodose ganglia were collected and fixed in 4% paraformaldehyde. 12 um tissue sections were then analyzed under a fluorescent microscope at 350nm and 555nm wavelength. Results In total, 27% of nodose cell bodies were labeled from the entire colon. Following proximal DiI injections, the percentage of labeled cell bodies in the nodose ganglia were 24.3± 3.9%. However, we observed a lower percentage of labeled neurons from the distal colon, with 9.3± 1.4% after DiI injections. FB labelling from the distal colon was three times less than that observed for DiI. Within the nodose ganglia, 40% of all distally labelled neurons were labelled with both tracers. Conclusions These findings indicate that in mice, both distal and proximal colon receives visceral sensory innervation from the vagus nerve. Thus, providing evidence for a sensory anatomical connection of the vagus nerve between these two parts of the colon. Funding Agencies CCC, CIHR

scholarly journals Major Lipids, Apolipoproteins, and Alterations of Gut Microbiota

2020 ◽  
Vol 9 (5) ◽  
pp. 1589
Author(s):  
Kyung Eun Yun ◽  
Jimin Kim ◽  
Mi-hyun Kim ◽  
Eunkyo Park ◽  
Hyung-Lae Kim ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
Large Scale ◽  
Blood Lipids ◽  
Density Lipoprotein ◽  
Lipoprotein Cholesterol ◽  
Control Group ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Lipid Markers

The gut microbiota has been linked to blood lipids. However, the relationship between the gut microbiome and other lipid markers like apolipoproteins A1 (apoA1) and B (apoB) as well as classical lipid markers in Asians remain unclear. Here, we examined the associations between gut microbial diversity and taxonomic compositions with both apolipoproteins and lipid markers in a large number of Korean patients. The fecal 16S rRNA gene sequencing data from 1141 subjects were analyzed and subjects were categorized into control group (G0) or abnormal group (G1) according to blood lipid measurements. The microbial diversity and several taxa of the gut microbiota were significantly associated with triglyceride, apoA1, and apoB levels, but not with total cholesterol, low-density lipoprotein cholesterol, and high-density lipoprotein cholesterol levels. The alpha diversity of the gut microbiota was inversely associated with high triglyceride level. Interestingly, G1 of apoA1 showed increased microbial richness and distinct microbial community compared with G0 of apoA1. A high abundance of Fusobacteria and low abundance of Oscillospira were found in the hypertriglyceridemia group. In this large-scale study, we identified associations of gut microbiota with apolipoproteins and classical lipid markers, indicating that the gut microbiota may be an important target for regulating blood lipids.

scholarly journals Epigenetic Changes Induced by Bacteroides fragilis Toxin

2019 ◽  
Vol 87 (6) ◽  
Author(s):  
Jawara Allen ◽  
Stephanie Hao ◽  
Cynthia L. Sears ◽  
Winston Timp
Keyword(s):  
Bacteroides Fragilis ◽  
Distal Colon ◽  
Chromatin Accessibility ◽  
Tumor Formation ◽  
Content Type ◽  
Intestinal Neoplasia ◽  
And Function ◽  
Gut Microbial Community ◽  
The Impact

ABSTRACT Enterotoxigenic Bacteroides fragilis (ETBF) is a Gram-negative, obligate anaerobe member of the gut microbial community in up to 40% of healthy individuals. This bacterium is found more frequently in people with colorectal cancer (CRC) and causes tumor formation in the distal colon of multiple intestinal neoplasia (Apcmin/+) mice; tumor formation is dependent on ETBF-secreted Bacteroides fragilis toxin (BFT). Because of the extensive data connecting alterations in the epigenome with tumor formation, initial experiments attempting to connect BFT-induced tumor formation with methylation in colon epithelial cells (CECs) have been performed, but the effect of BFT on other epigenetic processes, such as chromatin structure, remains unexplored. Here, the changes in gene expression (transcriptome sequencing [RNA-seq]) and chromatin accessibility (assay for transposase-accessible chromatin using sequencing) induced by treatment of HT29/C1 cells with BFT for 24 and 48 h were examined. Our data show that several genes are differentially expressed after BFT treatment and that these changes relate to the interaction between bacteria and CECs. Further, sites of increased chromatin accessibility are associated with the location of enhancers in CECs and the binding sites of transcription factors in the AP-1/ATF family; they are also enriched for common differentially methylated regions (DMRs) in CRC. These data provide insight into the mechanisms by which BFT induces tumor formation and lay the groundwork for future in vivo studies to explore the impact of BFT on nuclear structure and function.

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